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Cys-Cys Bond in the martinize.py script
- lihie
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12 years 4 months ago #860
by lihie
Cys-Cys Bond in the martinize.py script was created by lihie
Hello,
I wanted to ask if the option for Cys-Cys bond is working in the martinize.py script as specified in the script options " -cys Disulphide bond (+) ". I'm asking this because when I'm using the ngmx or the cg_bonds.tcl script to view the bonds- I don't see S-S bond.
Thank you,
Lihie
I wanted to ask if the option for Cys-Cys bond is working in the martinize.py script as specified in the script options " -cys Disulphide bond (+) ". I'm asking this because when I'm using the ngmx or the cg_bonds.tcl script to view the bonds- I don't see S-S bond.
Thank you,
Lihie
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- djurre
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12 years 4 months ago #863
by djurre
Replied by djurre on topic Cys-Cys Bond in the martinize.py script
The -cys options isn't explained very well indeed. There are three options: You can make martinize.py detect the cys-cys bonds by itself, using a standard cut-off (0.22nm):
-cys auto
This works well in most cases. The second option is to specify the cut-off yourself:
-cys 0.26
The third options would be to explicitly specify the residues between which a cys-bond has to be placed:
-cys A/CYS/26,A/CYS/84
where A is the chain of the residue, CYS is the residue name and 26 and 84 are the residue numbers. You can specify multiple cystine bonds by giving the -cys options multiple times:
-cys A/CYS/26,A/CYS/84 -cys A/CYS/34,A/CYS/93
I hope that helps. More documentation should be added soon.
-cys auto
This works well in most cases. The second option is to specify the cut-off yourself:
-cys 0.26
The third options would be to explicitly specify the residues between which a cys-bond has to be placed:
-cys A/CYS/26,A/CYS/84
where A is the chain of the residue, CYS is the residue name and 26 and 84 are the residue numbers. You can specify multiple cystine bonds by giving the -cys options multiple times:
-cys A/CYS/26,A/CYS/84 -cys A/CYS/34,A/CYS/93
I hope that helps. More documentation should be added soon.
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- lihie
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12 years 4 months ago #867
by lihie
Replied by lihie on topic Cys-Cys Bond in the martinize.py script
Hello Djurre,
Thank you for your reply. I tried to do it as you wrote in the third option, with the following command: ./martinize.py -f EGF2B_clean.pdb -o topol.top -x cg_EGF2B.pdb -ss EGF2B_SS.ssd -p backbone -nt -cys /CYS/2,/CYS/22 -cys /CYS/13,/CYS/25 -cys /CYS/27,/CYS/36 -cys /CYS/38,/CYS/68 -cys /CYS/51,/CYS/66 -cys /CYS/60,/CYS/71 -cys /CYS/73,/CYS/86 -cys /CYS/88,/CYS/109 -cys /CYS/93,/CYS/107 -cys /CYS/101,/CYS/112 -cys /CYS/114,/CYS/123 -cys /CYS/125,/CYS/148 -cys /CYS/132,/CYS/146 -cys /CYS/140,/CYS/151 -cys /CYS/153,/CYS/163 -cys /CYS/166,/CYS/169 -cys /CYS/173,/CYS/220 -cys /CYS/179,/CYS/200 -cys /CYS/182,/CYS/196 -cys /CYS/228,/CYS/252
But still no CYS-CYS bond are created (I checked in the protein.itp and also in the vmd with the cg_bonds.tcl script).
Did I write it wrong?
Lihie
Thank you for your reply. I tried to do it as you wrote in the third option, with the following command: ./martinize.py -f EGF2B_clean.pdb -o topol.top -x cg_EGF2B.pdb -ss EGF2B_SS.ssd -p backbone -nt -cys /CYS/2,/CYS/22 -cys /CYS/13,/CYS/25 -cys /CYS/27,/CYS/36 -cys /CYS/38,/CYS/68 -cys /CYS/51,/CYS/66 -cys /CYS/60,/CYS/71 -cys /CYS/73,/CYS/86 -cys /CYS/88,/CYS/109 -cys /CYS/93,/CYS/107 -cys /CYS/101,/CYS/112 -cys /CYS/114,/CYS/123 -cys /CYS/125,/CYS/148 -cys /CYS/132,/CYS/146 -cys /CYS/140,/CYS/151 -cys /CYS/153,/CYS/163 -cys /CYS/166,/CYS/169 -cys /CYS/173,/CYS/220 -cys /CYS/179,/CYS/200 -cys /CYS/182,/CYS/196 -cys /CYS/228,/CYS/252
But still no CYS-CYS bond are created (I checked in the protein.itp and also in the vmd with the cg_bonds.tcl script).
Did I write it wrong?
Lihie
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- djurre
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12 years 4 months ago #870
by djurre
Replied by djurre on topic Cys-Cys Bond in the martinize.py script
Does it work if you specify the chain: -cys A/CYS/2,A/CYS/22, even though there is know chain name present in the pdb file?
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- lihie
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12 years 4 months ago #871
by lihie
Replied by lihie on topic Cys-Cys Bond in the martinize.py script
I tried specify the chain as you wrote but still it did not work....
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- djurre
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12 years 4 months ago #873
by djurre
Replied by djurre on topic Cys-Cys Bond in the martinize.py script
That is strange. What happend is you let martinize detect the cystine bonds by it self (-cys auto)?
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- lihie
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12 years 4 months ago #874
by lihie
Replied by lihie on topic Cys-Cys Bond in the martinize.py script
Hi Dujjre,
It worked :-) Thank you very much, I hope everything else will work as well...
Lihie
It worked :-) Thank you very much, I hope everything else will work as well...
Lihie
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